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Atherosclerotic Plaque Macrophages Drive Abdominal Aortic Aneurysm Formation [bulkRNA-Seq]

GSE284251 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2025/03/06 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 13 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 13 samples: 6 × CS vs 5 × RA vs 2 × AAAGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Endothelial dysfunction drives atherosclerotic plaque macrophage-dependent abdominal aortic aneurysm formationNature immunology · 2025

Summary (written by the submitters)

There is no effective pharmacotherapy to prevent the growth and rupture of abdominal aortic aneurysms (AAA), a leading cause of death. We developed a novel preclinical model showing that the interaction of bona fide risk factors (i.e., cigarette smoke (CS) and hypercholesterolemia) induced AAA formation, rupture, and death. Elastin fragmentation resulted from CS-induced exacerbation of the atherosclerotic process, significant given atherosclerosis is a disease of the inner intimal layer of the artery, with the media remaining largely intact.

Read the full summary ↓

Importantly, arterial injury was driven by CSF-1-dependent macrophages (Mφ) accumulating within developing atherosclerotic plaques that exhibited tissue degrading proteolytic activity in vivo. Single-cell RNA sequencing further demonstrated conservation of Mφ responses in atherosclerotic plaque from murine and human AAA. Our findings advance understanding of the pathological sequelae of atherosclerosis, establishing plaque Mφ as important mediators of tissue damage and a potential target for prevention of AAA growth and rupture.

Published in

Endothelial dysfunction drives atherosclerotic plaque macrophage-dependent abdominal aortic aneurysm formation

Thayaparan D, Emoto T, Khan AB et al. · Nature immunology 2025 · PMID 40263614 · doi:10.1038/s41590-025-02132-8

This dataset

Open GSE284251 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE284251_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1198071 and SRA study SRP551367. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40263614) ↗

Study design

6 × CS vs 5 × RA vs 2 × AAA

Supports a between-group comparison across 13 samples.

How we read this: 3 replicated groups read from 13 sample titles; they account for 13 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8681009 AAA_R1 AAA
GSM8681010 AAA_R2 AAA
GSM8681011 CS_R1 CS
GSM8681012 CS_R2 CS
GSM8681013 CS_R3 CS
GSM8681014 CS_R4 CS
GSM8681015 CS_R5 CS
GSM8681016 CS_R6 CS
GSM8681017 RA_R1 RA
GSM8681018 RA_R2 RA
GSM8681019 RA_R3 RA
GSM8681020 RA_R4 RA
GSM8681021 RA_R5 RA

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